Bio-Formats importer and fluorescent video

Hi pals!

I've been trying to import large video files >4GB of calcium imaging created in Nikon's proprietary format. I only seem to be able to open the first image in the series via plot function. What I would like to do is open the video and be able to play it within the figure. I have previously been able to export to .avi and play it that way, but I lose all the associated metadata of the file. How would I be able to do this and maintain all the info?

Answer 1

[Prashant Arora]

Hi Douglas,

Have you tried using one of the following?

https://www.mathworks.com/help/images/ref/implay.html

https://www.mathworks.com/help/matlab/ref/videoreader.html

[Douglas Miller]

Indeed, however, the file format is .nd2 which wouldn't be compatible with the videoreader.

[Prashant Arora]

I don't believe MATLAB provides any documented function for importing nd2 file formats. There is a file exchange submission which can be worth trying. It mentions about supporting nd2 formats, but has not been updated in a while.

https://www.mathworks.com/matlabcentral/fileexchange/32920-imread-for-multiple-life-science-image-file-formats

It also references the original source, which might have an up-to-date code.

https://www-legacy.openmicroscopy.org/site/support/bio-formats5.5/developers/matlab-dev.html